Publications
- Original samtools variant calling (
bcftools call -c) -
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 27(21) 2987-93. link
- BAQ calculation
-
Li H. Improving SNP discovery by base alignment quality. Bioinformatics (2011) 27(8):1157-8. link
- Detecting runs of homozygozity (
bcftools roh) -
Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, and Durbin R. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics (2016) 32(11) 1749-51 link
- CNV calling (
bcftools cnvandbcftools polysomy) -
Danecek P, McCarthy SA, HipSci Consortium, and Durbin R. A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data, PLoS One (2016) 11(5) e0155014 link
- Consequence calling (
bcftools csq) -
Danecek P, McCarthy SA. BCFtools/csq: Haplotype-aware variant consequences. Bioinformatics (2017) 33(13) 2037-39 link
- All of BCFtools, file manipuplation,
-mcalling, etc -
Danecek P, Bonfield JK, et al. Twelve years of SAMtools and BCFtools. Gigascience (2021) 10(2):giab008 link
Various math notes
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